Physical Principles in Nucleic Acid Chemistry

David E. Draper, Johns Hopkins University, Department of Chemistry / Department of Biophysics.

Nucleic acid structure. The building blocks of nucleic acid structure. DNA helices and non-canonical structures. RNA secondary and tertiary structure. Energetics of forming DNA and RNA structures. Thermodynamics of secondary structure formation in DNA and RNA. Salt and the stability of duplex DNA. Thermodynamics and kinetics of RNA tertiary structure formation. DNA flexibility: bending, twisting, and supercoiling. Non-specific DNA binding. Specific DNA sequence recognition. RNA binding proteins. Small molecule — nucleic acid interactions. Manipulation of nucleic acids by proteins and protein complexes. Appendix.